Unraveling Exciton-Plasmon Coupling and the PIRET Mechanism in Decorated Silicon Nanowires.

Exciton-plasmon coupling is a fascinating physical phenomenon that has been investigated in various metal semiconductor systems. Intentionally chosen silicon nanowires (SiNWs) systems act as a host material for providing exciton as well as silicon oxide as a thin dielectric. A clear blue-shift in photoluminescence (PL) peak and a significant increase in visible range absorption were observed for metal nanoparticle (MNP) decorated SiNWs (D-SiNWs) which signifies the presence of exciton-plasmon coupling. A further investigation reveals that the possibility of the occurrence of the plasmon-induced resonance energy transfer (PIRET) mechanism is higher. The PL intensity enhancement in Au-decorated SiNWs is higher (∼38 times) in comparison to that in Pt due to the presence of a strong and localized electric field of plasmons near the interface of metal and semiconductors. Moreover, splitting in PL for gold-decorated SiNWs might be due to the presence of dipole-quadrupole coupling along with dipole-dipole coupling, which further increases the strength of the PIRET mechanism.

Implications of In Vitro Multi-Serine Phosphorylation of Alpha-Synuclein in Aggregation and Cytotoxicity.

Post-translational modifications guide the functional diversity and identity of proteins. Phosphorylation is one such post-translational modification that has been reported in pathological proteins related to various neurodegenerative disorders such as α-synuclein (α-syn) phosphorylation in Parkinson's disease and other synucleinopathies. In α-syn, the phosphorylation has mostly been observed at S129; however, the occurrence of other serine modifications at S9, S42, and S87 is partially explored. In pathogenic conditions, where α-syn is phosphorylated by complex kinase pathways, multi-site modifications may happen and alter the mechanism of α-syn aggregation. Here, using Polo-like kinase 2 and G-protein coupled receptor kinase 4, the in vitro phosphorylation of α-syn was performed, which revealed multi-serine phosphorylation. Mass spectrometry with customized proteolytic digestion showed prominent phosphorylation at S129 and modifications at S87 and S42 with PLK2 and S87 with GRK4. The phosphorylation at the identified serine residues was further validated with NMR and western blotting. Multi-serine phosphorylation aggravates the aggregation potential of monomeric α-syn, seeding capacity, and cytotoxicity in the SH-SY5Y cell line. This study proposes evidence for in vitro multi-site phosphorylation and its significance in α-syn aggregation, toxicity, and related pathogenesis.

A natural small molecule-mediated inhibition of alpha-synuclein aggregation leads to neuroprotection in Caenorhabditis elegans.

Small molecules are being explored intensively for their applications as therapeutic molecules in the management of metabolic and neurological disorders. The natural small molecules can inhibit protein aggregation and underlying cellular pathogenesis of neurodegenerative diseases involving multi-factorial mechanisms of action. Certain natural small molecular inhibitors of pathogenic protein aggregation are highly efficient and have shown promising therapeutic potential. In the present study, Shikonin (SHK), a natural plant-based naphthoquinone has been investigated for its aggregation inhibition activity against α-synuclein (α-syn) and the neuroprotective potential in Caenorhabditis elegans (C. elegans). SHK significantly inhibited aggregation of α-syn at sub-stochiometric concentrations, delayed the linear lag phase and growth kinetics of seeded and unseeded α-syn aggregation. The binding of SHK to the C-terminus of α-syn maintained α-helical and disordered secondary structures with reduced beta-sheet content and complexity of aggregates. Further, in C. elegans transgenic PD models, SHK significantly reduced α-syn aggregation, improved locomotor activity and prevented dopaminergic (DA) neuronal degeneration, indicating the neuroprotective role of SHK. The present study highlights the potential of natural small molecules in the prevention of protein aggregation that may further be explored for their therapeutic efficacy in the management of protein aggregation and neurodegenerative diseases.

Bisphenol-A (BPA) Impairs Hippocampal Neurogenesis via Inhibiting Regulation of the Ubiquitin Proteasomal System.

The ubiquitin-proteasome system (UPS) controls protein homeostasis to maintain cell functionality and survival. Neurogenesis relies on proteasome function, and a defective proteasome system during brain development leads to neurological disorders. An endocrine-disrupting xenoestrogen bisphenol-A (BPA) used in plastic products adversely affects human health and causes neurotoxicity. Previously, we reported that BPA reduces neural stem cells (NSCs) proliferation and differentiation, impairs myelination and mitochondrial protein import, and causes excessive mitochondrial fragmentation leading to cognitive impairments in rats. Herein, we examined the effect(s) of prenatal BPA exposure on UPS functions during NSCs proliferation and differentiation in the hippocampus. Rats were orally treated with 40 µg/kg body weight BPA during day 6 gestation to day 21 postnatal. BPA significantly reduced proteasome activity in a cellular extract of NSCs. Immunocytochemistry exhibited a significant reduction of 20S proteasome/Nestin+ and PSMB5/Nestin+ cells in NSCs culture. BPA decreased 20S/Tuj1+ and PSMB5/Tuj1+ cells, indicating disrupted UPS during neuronal differentiation. BPA reduced the expression of UPS genes, 20S, and PSMB5 protein levels and proteasome activity in the hippocampus. It significantly reduced overall protein synthesis by the loss of Nissl substances in the hippocampus. Pharmacological activation of UPS by a bioactive triterpenoid 18α-glycyrrhetinic acid (18α GA) caused increased proteasome activities, significantly increased neurosphere size and number, and enhanced NSCs proliferation in BPA exposed culture, while proteasome inhibition by MG132 further aggravates BPA-mediated effects. In silico studies demonstrated that BPA strongly binds to catalytic sites of UPS genes (PSMB5, TRIM11, Parkin, and PSMD4) which may result in UPS inactivation. These results suggest that BPA significantly reduces NSCs proliferation by impairing UPS, and UPS activation by 18α GA could suppress BPA-mediated neurotoxicity and exerts neuroprotection.

Differential interactions of α-synuclein conformers affect refolding and activity of proteins.

The accumulation of protein aggregates as intracellular inclusions interferes with cellular protein homeostasis leading to protein aggregation diseases. Protein aggregation results in the formation of several protein conformers including oligomers and fibrils, where each conformer has its own structural characteristic and proteotoxic potential. The present study explores the effect of alpha-synuclein (α-syn) conformers on the activity and spontaneous refolding of firefly luciferase. Of the different conformers, α-syn monomers delayed the inactivation of luciferase under thermal stress conditions and enhanced the spontaneous refolding of luciferase. In contrast, the α-syn oligomers and fibrils adversely affected luciferase activity and refolding, where the oligomers inhibited spontaneous refolding, whereas a pronounced effect on the inactivation of native luciferase was observed in the case of fibrils. These results indicate that the oligomers and fibrils of α-syn interfere with the refolding of luciferase and promote its misfolding and aggregation. The study reveals the differential propensities of various conformers of a pathologically relevant protein in causing inactivation, structural modifications and misfolding of other proteins, consequently resulting in altered protein homeostasis.

X-ray radiation monitor for measuring solids content in fluid fine tailings.

The extraction of bitumen from oil sands produces fluid fine tailings (FFT) consisting mainly of water, sands, clay, and residual bitumen. Generally, devices with radioactive sources are used to measure the variation of FFT density or solids concentration inline, but to date there is no suitable device for in situ monitoring in tailings storage facilities such as large tailings ponds. In this study, an alternative method using high-resolution spectrometry based on a low radiation intensity source and a cadmium telluride (CdTe) detector was used to measure the solids content in tailings samples based on X-ray attenuation. The radiation source used in the experiment was a 1 µCi 133 Ba. GEANT4, a Monte Carlo-based simulation code that calculates the transmission of radiation through matter, was used to simulate the results of this study and build calibration curves that can determine the solids content concentration based on measured sample composition. Experiments and simulations were performed on various concentrations of both actual FFT samples from tailings facilities and kaolin as a model material. Good agreement between the experimental and simulation results was observed, paving the way for a potential real-time solids content measurement system that could be deployed over large areas to measure the settling of FFT in tailings ponds.

A real-time light-scattering technique for tailings solids measurement.

This study presents the concept of an economic in situ light-scattering sensor for real-time measurement of the solid content in tailings facilities. An experimental setup using a blue (405 nm wavelength) laser diode and silicon photodiodes was constructed to measure the angular distribution of the intensity of scattered light. It was found that the angular intensity of scattered light for tailing samples follows a cosn (θ) relation with n ≈ 1.5, where θ is the angle between the laser beam and the photodiode. An angular value of θ = 20° was chosen for the sensor design based on a high signal-to-noise ratio. The setup was used to determine the relation between scattered light intensity and solids content using a thickened tailings underflow from an oil sands facility and Kaolin as a model material. It was observed that the intensity of scattered light tends to increase with an increase in solids content, with qualitatively similar settling behavior for the two materials but at largely different time scales. An insertion-based prototype was built and tested in a large (2.7 m height) settling column with treated mature fine tailings, and the light-scattering data were verified by standard gravimetric method and gamma-ray measurements. In general, good agreement was established between these measurements in the absence of optical fouling, which demonstrates the potential of the sensor as an effective tool for tailings management.

Identification of Natural Products as Potential Pharmacological Chaperones for Protein Misfolding Diseases.

Defective protein folding and accumulation of misfolded proteins is associated with neurodegenerative, cardiovascular, secretory, and metabolic disorders. Efforts are being made to identify small-molecule modulators or structural-correctors for conformationally destabilized proteins implicated in various protein aggregation diseases. Using a metastable-reporter-based primary screen, we evaluated pharmacological chaperone activity of a diverse class of natural products. We found that a flavonoid glycoside (C-10, chrysoeriol-7-O-ß-D-glucopyranoside) stabilizes metastable proteins, prevents its aggregation, and remodels the oligomers into protease-sensitive species. Data was corroborated with additional secondary screen with disease-specific pathogenic protein. In vitro and cell-based experiments showed that C-10 inhibits α-synuclein aggregation which is implicated in synucleinopathies-related neurodegeneration. C-10 interferes in its structural transition into ß-sheeted fibrils and mitigates α-synuclein aggregation-associated cytotoxic effects. Computational modeling suggests that C-10 binds to unique sites in α-synuclein which may interfere in its aggregation amplification. These findings open an avenue for comprehensive SAR development for flavonoid glycosides as pharmacological chaperones for metastable and aggregation-prone proteins implicated in protein conformational diseases.

Pesticide interactions induce alterations in secondary structure of malate dehydrogenase to cause destability and cytotoxicity.

Environmental exposure to pesticides increases the risk of neurotoxicity and neurodegenerative diseases. The mechanism of pesticide-induced toxicity is attributed to the increased reactive oxygen species, mitochondrial dysfunction, inhibition of key cellular enzymes and accelerated pathogenic protein aggregation. The structural basis of pesticide-protein interaction is limited to pathogenic proteins such as α-synuclein, Tau and amyloid-beta. However, the effect of pesticides on metabolic proteins is still unexplored. Here, we used rotenone and chlorpyrifos to understand the interaction of these pesticides with a metabolic protein, malate dehydrogenase (MDH) and the consequent pesticide-induced cytotoxicity. We found that rotenone and chlorpyrifos strongly bind to MDH, interferes with protein folding and triggers alteration in its secondary structure. Both pesticides showed high binding affinities for MDH as observed by NMR and LCMS. Rotenone and chlorpyrifos induced structural alterations during MDH refolding resulting in the formation of cytotoxic conformers that generated oxidative stress and reduced cell viability. Our findings suggest that pesticides, in general, interact with proteins resulting in the formation of cytotoxic conformers that may have implications in neurotoxicity and neurodegenerative diseases.

Fast kinetics of environmentally induced α-synuclein aggregation mediated by structural alteration in NAC region and result in structure dependent cytotoxicity.

Aggregation of α-synuclein (α-syn) is associated with the manifestation of various pathogenic synucleinopathies, including Parkinson's disease attributed to both genetic and environmental stress factors. The initial events triggering α-syn aggregation and disease initiation due to environmental stress factors are still largely unknown. Here, to understand the mechanism of misfolding and aggregation initiation, we induced α-syn aggregation with rotenone, an established chemical inducer of PD like symptoms. We found that rotenone accelerates the formation of structurally distinct oligomers and fibrils that act as templates and increase the formation of conformers capable of spreading to the neighboring neuronal cells. Molecular dynamics simulations and NMR studies revealed the involvement of NAC region and formation of helical conformations resulting in structural variations in oligomers and fibrils. These structural variations affect the cytotoxic potential of oligomers and fibrils, where, the beta sheet rich oligomers and fibrils alter the membrane potential of neuronal cells and lead to early apoptosis. Our results describe the initial mechanistic events in pathogenic protein aggregation, where initial structural alterations in response to external stress factors dictate the toxicity of resulting conformers. This information will further provide insights in the understanding of protein aggregation, disease progression and pathogenesis.

Western Indian Rural Gut Microbial Diversity in Extreme Prakriti Endo-Phenotypes Reveals Signature Microbes.

Heterogeneity amidst healthy individuals at genomic level is being widely acknowledged. This, in turn, is modulated by differential response to environmental cues and treatment regimens, necessitating the need for stratified/personalized therapy. We intend to understand the molecular determinants of Ayurvedic way (ancient Indian system of medicine) of endo-phenotyping individuals into distinct constitution types termed "Prakriti," which forms the basis of personalized treatment. In this study, we explored and analyzed the healthy human gut microbiome structure within three predominant Prakriti groups from a genetically homogenous cohort to discover differentially abundant taxa, using 16S rRNA gene based microbial community profiling. We found Bacteroidetes and Firmicutes as major gut microbial components in varying composition, albeit with similar trend across Prakriti. Multiple species of the core microbiome showed differential abundance within Prakriti types, with gender specific signature taxons. Our study reveals that despite overall uniform composition of gut microbial community, healthy individuals belonging to different Prakriti groups have enrichment of specific bacteria. It highlights the importance of Prakriti based endo-phenotypes to explain the variability amongst healthy individuals in gut microbial flora that have important consequences for an individual's health, disease and treatment.

Effect of ionic size compensation by Ag+ incorporation in homogeneous Fe-substituted ZnO: studies on structural, mechanical, optical, and magnetic properties.

Substituting an ion of different size from that of the host element introduces lattice strain and defects. However, this mismatch may be significantly reduced by substituting an additional ion with a compensating size relative to the dopant. Such a double substitution might offer better solubility irrespective of the local distortions as well as the formation of defects in the valence states. Fe-substituted ZnO has been widely reported with conflicting results primarily arising from lack of chemical and structural homogeneity originating from preparation techniques, compositional fluctuations, and equivocal comprehension of actual solubility limits of the dopants. In this study, Ag ion has been incorporated in Fe-substituted ZnO to compensate the ionic size of Zn1-x [Fe0.8Ag0.2] x O (0 ≤ x ≤ 0.03125) by determining the solubility limit of the homogeneous material and their corresponding structural, mechanical, optical and magnetic properties have been investigated thoroughly. Co-substitution rearranges the lattice and leads to better crystal structures with tunable properties related to the amount of substitution.

Correction: Effect of ionic size compensation by Ag+ incorporation in homogeneous Fe-substituted ZnO: studies on structural, mechanical, optical, and magnetic properties.

[This corrects the article DOI: 10.1039/C8RA02393J.].

Structural Distortion and Bandgap Increment in Nanocrystalline Wurtzite Si Substituted ZnO.

Crystalline Zn(1−x) Si(x) O(0 ≤ x ≤ 0.156) nanoparticles reveal decreasing particle size with increasing Si content and a undistorted wurtzite form until x = 0.062 beyond which local deformation is observed maintaining the parent structure. There is a sharp increment in bandgap with nominal Si-doping and then almost saturates onwards. Moreover thermal annealing demonstrate the increase bandgap and decreasing lattice parameters. The details of samples synthesis and characterization is presented in the present manuscript.

Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes.

Numerous microbes inhabit the human intestine, many of which are uncharacterized or uncultivable. They form a complex microbial community that deeply affects human physiology. To identify the genomic features common to all human gut microbiomes as well as those variable among them, we performed a large-scale comparative metagenomic analysis of fecal samples from 13 healthy individuals of various ages, including unweaned infants. We found that, while the gut microbiota from unweaned infants were simple and showed a high inter-individual variation in taxonomic and gene composition, those from adults and weaned children were more complex but showed a high functional uniformity regardless of age or sex. In searching for the genes over-represented in gut microbiomes, we identified 237 gene families commonly enriched in adult-type and 136 families in infant-type microbiomes, with a small overlap. An analysis of their predicted functions revealed various strategies employed by each type of microbiota to adapt to its intestinal environment, suggesting that these gene sets encode the core functions of adult and infant-type gut microbiota. By analysing the orphan genes, 647 new gene families were identified to be exclusively present in human intestinal microbiomes. In addition, we discovered a conjugative transposon family explosively amplified in human gut microbiomes, which strongly suggests that the intestine is a 'hot spot' for horizontal gene transfer between microbes.

Effect of temperature on oviposition in four species of the melanogaster group of Drosophila

Experiments were conducted to test the effect of temperature on oviposition in four species of the melanogaster group of Drosophila: D. ananassae, D. bipectinata, D. malerkotliana and D. biarmipes. In each species, two wild strains were used and eggs laid by females at three different temperatures (19 degrees C, 24 degrees C and 30 degrees C) were counted for four days at 24 h interval. It is evident from the results that females of D. ananassae, D. bipectinata, D. malerkotliana and D. biarmipes lay low number of eggs at low temperature (19 degrees C). Thus oviposition in these four species of Drosophila is significantly reduced at low temperature.